MolNFT v1 · #129435 · protein
High resolution structure of native GAN1D, a putative 6-phospho-beta- galactosidase from geobacillus stearothermophilus
5OKB · Putative 6-phospho-beta-galactobiosidase: “High resolution structure of native GAN1D, a putative 6-phospho-beta- galactosidase from geobacillus…”. X-ray diffraction, 1 ligand (PO4), 16 pockets (best druggability 0.87). MolNFT v1…
- PDB
- 5OKB
- Type
- protein
- Length
- 1,878 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative 6-phospho-beta-galactobiosidase
- EC
- 3.2.1.85
- UniProt
- W8QF82
- Ligands
- PO4
- Pockets
- 16 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative 6-phospho-beta-galactobiosidase (EC 3.2.1.85) | protein | 475 | 41% helix, 16% strand | W8QF82 |
| B, C | Putative 6-phospho-beta-galactobiosidase (EC 3.2.1.85) | protein | 474 | 41% helix, 16% strand | W8QF82 |
| D | Putative 6-phospho-beta-galactobiosidase (EC 3.2.1.85) | protein | 455 | 43% helix, 18% strand | W8QF82 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 4 copies · chains A, B, C, D
- IMD · Imidazole · additive · 8 copies · chains A, B, D, C
- GOL · Glycerol · additive · 2 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1147 | 0.87 | 0.88 | 103 | IMD, PO4 |
| 2 | 966 | 0.84 | 0.86 | 82 | PO4 |
| 3 | 1175 | 0.83 | 0.84 | 81 | IMD, PO4 |
| 4 | 145 | 0.81 | 0.98 | 27 | empty |
| 5 | 134 | 0.80 | 0.98 | 21 | empty |
Interfaces
4 interfaces between chains.
- B–D · 1609 Ų buried · 30 hydrogen bonds · protein-protein
- A–C · 1609 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 511 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 243 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5OKB · High resolution structure of native Gan1D, a putative 6-phospho-beta-galactosidase from… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt W8QF82
- Elsewhere: RCSB PDB 5OKB · PDBe 5OKB · UniProt W8QF82
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